tbuckley/cabot-search huggingface dataset:
Tensor Decomposition-based Feature Extraction and Classification to Detect Natural Selection from Genomic Data
Authors: Md Ruhul Amin, Mahmudul Hasan, Sandipan Paul Arnab, Michael DeGiorgio
Journal: Molecular Biology and Evolution (2023)

Abstract Inferences of adaptive events are important for learning about traits, such as human digestion of lactose after infancy and the rapid spread of viral variants. Early efforts toward identifying footprints of natural selection from genomic data involved development of summary statistic and likelihood methods. However, such techniques are grounded in simple patterns or theoretical models that limit the complexity of settings they can explore. Due to the renaissance in artificial intelligence, machine learning methods have taken center stage in recent efforts to detect natural selection, with strategies such as convolutional neural networks applied to images of haplotypes. Yet, limitations of such techniques include estimation of large numbers of model parameters under nonconvex settings and feature identification without regard to location within an image. An alternative approach is to use tensor decomposition to extract features from multidimensional data although preserving the latent structure of the data, and to feed these features to machine learning models. Here, we adopt this framework and present a novel approach termed T-REx, which extracts features from images of haplotypes across sampled individuals using tensor decomposition, and then makes predictions from these features using classical machine learning methods. As a proof of concept, we explore the performance of T-REx on simulated neutral and selective sweep scenarios and find that it has high power and accuracy to discriminate sweeps from neutrality, robustness to common technical hurdles, and easy visualization of feature importance. Therefore, T-REx is a powerful addition to the toolkit for detecting adaptive processes from genomic data.
Impact of <scp>COVID</scp>‐19 in patients with heart failure with mildly reduced or preserved ejection fraction enrolled in the <scp>DELIVER</scp> trial
Authors: Ankeet S. Bhatt, Mikhail N. Kosiborod, Brian L. Claggett, Zi Michael Miao, Muthiah Vaduganathan, Carolyn S.P. Lam, Adrian F. Hernandez, Felipe A. Martinez, Silvio E. Inzucchi, Sanjiv J. Shah, Rudolf A. de Boer, Pardeep S. Jhund, Akshay S. Desai, James C. Fang, Yaling Han, Josep Comin‐Colet, Jarosław Drożdż, Orly Vardeny, Bela Merkely, Daniel Lindholm, Magnus Peterson, Anna Maria Langkilde, John J.V. McMurray, Scott D. Solomon
Journal: European Journal of Heart Failure (2023)

COVID-19 may affect clinical risk in patients with heart failure. DELIVER began before and was conducted during the COVID-19 pandemic. This study aimed to evaluate the association between COVID-19 and clinical outcomes among DELIVER participants.
Incorporating Effects of Time Accrued on the Waiting List into Lung Transplantation Survival Models
Authors: Jarrod E. Dalton, Paul R. Gunsalus, Carli J. Lehr, Johnie Rose, Belinda L. Udeh, Maryam Valapour
Journal: American Journal of Respiratory and Critical Care Medicine (2023)

U.S. lung transplant mortality risk models do not account for patients' disease progression as time accrues between mandated clinical parameter updates.
Incremental prognostic value of intensity-weighted regional calcification scoring using contrast CT imaging in TAVR
Authors: Mohamed Abdelkhalek, Nikrouz Bahadormanesh, Javier Ganame, Zahra Keshavarz-Motamed
Journal:  (2023)

Abstract Aims Aortic valve calcification scoring plays an important role in predicting outcomes of transcatheter aortic valve replacement (TAVR). However, the impact of relative calcific density and its causal effect on peri-procedural complications due to sub-optimal valve expansion remains limited. This study aims to investigate the prognostic power of quantifying regional calcification in the device landing zone in the context of peri-procedural events and post-procedural complications based on pre-operative contrast computed tomography angiography (CCTA) images. Assess the effect of calcification on post-procedural device expansion and final configuration. Methods and results We introduce a novel patient invariant topographic scheme for quantifying the location and relative density of landing zone calcification. The calcification was detected on CCTA images based on a recently developed method using automatic minimization of the false positive rate between aortic lumen and calcific segments. Multinomial logistic regression model evaluation and ROC curve analysis showed excellent classification power for predicting paravalvular leakage [area under the curve (AUC) = 0.8; P &amp;lt; 0.001] and balloon pre-dilation (AUC = 0.907; P &amp;lt; 0.001). The model exhibited an acceptable classification ability for left bundle branch block (AUC = 0.748; P &amp;lt; 0.001) and balloon post-dilation (AUC = 0.75; P &amp;lt; 0.001). Notably, all evaluated models were significantly superior to alternative models that did not include intensity-weighted regional volume scoring. Conclusions TAVR planning based on contrast computed tomography images can benefit from detailed location, quantity, and density contribution of calcific deposits in the device landing zone. Those parameters could be employed to stratify patients who need a more personalized approach during TAVR planning, predict peri-procedural complications, and indicate patients for follow-up monitoring.
Chronic intestinal schistosomiasis caused by co-infection with Schistosoma intercalatum and Schistosoma mansoni
Authors: Przemysław Kołodziej, Beata Szostakowska, Anna Lass, Małgorzata Sulima, Katarzyna Sikorska, Janusz Kocki, Witold Krupski, Dorota Starownik, Paweł Bojar, Justyna Szumiło, Beata Kasztelan-Szczerbińska, Halina Cichoż-Lach, Jacek Bogucki, Magdalena Szymańska, Hanna Fota-Markowska, Anna Bogucka-Kocka
Journal: The Lancet Infectious Diseases (2023)

The Grand Round concerns a 24-year-old man from Zimbabwe who was studying and living in Poland. The patient had been complaining of abdominal pain, fatigue, alternating diarrhoea and constipation, and presence of blood in his stool for 3 years. The patient had the following diagnostic tests: colonoscopy, CT scan, histopathology, and parasitological and molecular tests. Results of the examinations showed that the cause of the patient's complaints was chronic intestinal schistosomiasis due to the co-infection with Schistosoma intercalatum and Schistosoma mansoni. The patient had two cycles of praziquantel therapy (Biltricide) and responded well to the treatment. In the Grand Round, we describe full diagnostics as well as clinical and therapeutic management in the patient with S intercalatum and S mansoni co-infection. This case allows us to draw attention to cases of forgotten chronic tropical diseases (including rare ones) in patients from regions with a high endemic index staying in non-endemic regions of the world for a long time. Co-infection with S intercalatum and S mansoni should be considered as a very rare clinical case.
Efficacy, safety, tolerability, and pharmacokinetics of long-acting injectable cabotegravir for HIV pre-exposure prophylaxis in transgender women: a secondary analysis of the HPTN 083 trial
Authors: Mark A Marzinke, Brett Hanscom, Zhe Wang, Steven A Safren, Christina Psaros, Deborah Donnell, Paul A Richardson, Philip Sullivan, Susan H Eshleman, Andrea Jennings, Kailazarid Gomez Feliciano, Emilia Jalil, Carolina Coutinho, Nadir Cardozo, Bernardo Maia, Taimur Khan, Yashna Singh, Keren Middelkoop, Julie Franks, Javier Valencia, Naiymah Sanchez, Jonathan Lucas, James F Rooney, Alex R Rinehart, Susan Ford, Adeola Adeyeye, Myron S Cohen, Marybeth McCauley, Raphael J Landovitz, Beatriz Grinsztejn, Suwat Chariyalertsak, Chaiwat Ungsedhapand, Nittaya Phanuphak, Tran Viet Ha, María Inés Figueroa, Marcelo H. Losso, Esper G. Kallas, José Valdez Madruga, Breno Riegel Santos, Beatriz Grinsztejn, Juan Carlos Hinojosa Boyer, Milagros Erika Matta Aguirre, Jorge A Gallardo-Cartagena, Javier Valencia, Yvett Pinedo Ramirez, Keren Middelkoop, Paul Goepfert, Sybil Hosek, Albert Liu, Jessica Justman, Christopher Hurt, Daniel Reirden, Carl Fichtenbaum, Christopher Hall, Kenneth Mayer, Manya Magnus, Cornelius van Dam, Julie Franks, Colleen Kelley, Roberto C. Arduino, Anne Rompalo, Shobha Swaminathan, Sue Ellen Abdalian, Hong Van Tieu, Jose Bazan, Ian Frank, Carlos del Rio, Aditya Gaur, Raphael J. Landovitz, Jesse Clark, Richard Novak, Rachel Presti, Roy (Trip) Gulick
Journal: The Lancet HIV (2023)
Immunogenicity and safety of AZD2816, a beta (B.1.351) variant COVID-19 vaccine, and AZD1222 (ChAdOx1 nCoV-19) as third-dose boosters for previously vaccinated adults: a multicentre, randomised, partly double-blinded, phase 2/3 non-inferiority immunobridging study in the UK and Poland
Authors: Maheshi N Ramasamy, Elizabeth J Kelly, Seth Seegobin, Paul I Dargan, Ruth Payne, Vincenzo Libri, Matthew Adam, Parvinder K Aley, Nuria Martinez-Alier, Alison Church, Brett Jepson, Mark Khan, Sam Matthews, G Todd Townsend, Johan Vekemans, Sagida Bibi, Phillip A Swanson, Teresa Lambe, Menelas N Pangalos, Tonya Villafana, Andrew J Pollard, Justin A Green, Eden Wildman, Tommy Rampling, Sheila Morris, Kathryn Shoemaker, Anastasia Aksyuk, Marcelino Giune Padilla, Tiffany Roe, Christos J Petropoulos, Terri Wrin, Hayley Colton, Karen Bisnauthsing, Catherine Smith, Lucy Leeman, James Galloway, Deepak Nagra, Rajeka Lazarus, Florentina Penciu, Ewan Hunter, Anju Sahdev, David Turner, Simon Royal, Alison Uriel, Andrew Ustianowski, Ed Moran, Christopher Green, Amisha Desai, Nicki Lakeman, Patrick Moore, Ashley Whittington, Iwona Kobielusz Gembala, Marek Konieczny
Journal: The Lancet Microbe (2023)

This study aimed to evaluate AZD2816, a variant-updated COVID-19 vaccine expressing the full-length SARS-CoV-2 beta (B.1.351) variant spike protein that is otherwise similar to AZD1222 (ChAdOx1 nCoV-19), and AZD1222 as third-dose boosters.
Geometry of cold snare polypectomy and risk of incomplete resection
Authors: Oliver Cronin, David Kirszenblat, Nauzer Forbes, Sunil Gupta, Anthony Whitfield, Timothy O'Sullivan, Julia Gauci, Muhammad Abuarisha, Hunter Wang, Nicholas G. Burgess, Eric Y.T. Lee, Stephen J. Williams, Michael J. Bourke
Journal: Endoscopy (2023)

Abstract Background Cold snare polypectomy (CSP) is safer than and equally efficacious as hot snare polypectomy (HSP) for the removal of small (&lt;10mm) colorectal polyps. The maximum polyp size that can be effectively managed by piecemeal CSP (p-CSP) without an excessive burden of recurrence is unknown. Methods Resection error risks (RERs), defined as the estimated likelihood of incomplete removal of adenomatous tissue for a single snare resection pass, for CSP and HSP were calculated, based on an incomplete resection rate. Polyp area, snare size, estimated number of resections, and optimal resection defect area were modeled. Overall risk of incomplete resection (RIR) was defined as RIR=1 – (1 – p)n, where p is the RER and n the number of resections. Results A 40-mm polyp has a four times greater area than a 20-mm polyp (314.16mm2 vs. 1256.64mm2), and requires three times more resections (11 vs. 33, respectively, assuming 8-mm piecemeal resection pieces for p-CSP). RIRs for a 40-mm polyp by HSP and p-CSP were 15.1%–23% and 40.74%–60.60% respectively. Conclusion RER is more important with p-CSP than with HSP. The number of resections, n, and consequently RIR increases with increasing polyp size. Given the overwhelming safety of CSP, specific techniques to minimize the RER should be studied and developed.
Reply to Yasuma <i>et al</i>.
Authors: Allison E. Norlander, Masako Abney, Jacqueline-Yvonne Cephus, Caroline E. Roe, Jonathan M. Irish, Nicholas J. Shelburne, Dawn C. Newcomb, Anna R. Hemnes, R. Stokes Peebles
Journal: American Journal of Respiratory and Critical Care Medicine (2023)

"Reply to: Epoprostenol and Treprostinil: Differential Effects on Regulatory T Cell Generation in Patients with Pulmonary Arterial Hypertension." American Journal of Respiratory and Critical Care Medicine, 0(ja), pp.
Epoprostenol and Treprostinil: Differential Effects on Regulatory T-Cell Generation in Patients with Pulmonary Arterial Hypertension
Authors: Taro Yasuma, Hajime Fujimoto, Corina N. D’Alessandro-Gabazza, Esteban C. Gabazza, Osamu Hataji, Tetsu Kobayashi
Journal: American Journal of Respiratory and Critical Care Medicine (2023)

"Epoprostenol and Treprostinil: Differential Effects on Regulatory T Cell Generation in Patients with Pulmonary Arterial Hypertension." American Journal of Respiratory and Critical Care Medicine, 0(ja), pp.
The clinical and financial burden of nonhepatocellular carcinoma focal lesions detected during the surveillance of patients with cirrhosis
Authors: Pierre Nahon, Richard Layese, Nathalie Ganne-Carrié, Cécile Moins, Gisèle N’Kontchou, Cendrine Chaffaut, Maxime Ronot, Etienne Audureau, Isabelle Durand-Zaleski, Pierre-André Natella
Journal: Hepatology (2023)

Background and Aims: HCC surveillance is challenged by the detection of hepatic focal lesions (HFLs) of other types. This study aimed to describe the incidence, characteristics, outcomes, and costs of non-HCC HFL detected during surveillance. Approach and Results: We retrospectively analyzed nonstandardized workup performed in French patients included in HCC surveillance programs recruited in 57 French tertiary centers (ANRS CirVir and CIRRAL cohorts, HCC 2000 trial). The overall cost of workup was evaluated, with an estimation of an average cost per patient for the entire population and per lesion detected. A total of 3295 patients were followed up for 59.8 months, 391 (11.9%) patients developed HCCs (5-year incidence: 12.1%), and 633 (19.2%) developed non-HCC HFLs (5-year incidence: 21.8%). Characterization of non-HCC HFL required a median additional of 0.7 exams per year. A total of 11.8% of non-HCC HFLs were not confirmed on recall procedures, and 19.6% of non-HCC HFLs remained undetermined. A definite diagnosis of benign liver lesions was made in 65.1%, and malignant tumors were diagnosed in 3.5%. The survival of patients with benign or undetermined non-HCC HFL was similar to that of patients who never developed any HFL (5-year survival 92% vs. 88%, p = 0.07). The average cost of the diagnostic workup was 1087€ for non-HCC HFL and €1572 for HCC. Conclusions: Non-HCC HFLs are frequently detected in patients with cirrhosis, and do not impact prognosis, but trigger substantial costs. This burden must be considered in cost-effectiveness analyses of future personalized surveillance strategies.
Spatial mapping of human hematopoiesis at single-cell resolution reveals aging-associated topographic remodeling
Authors: Aleksandr Sarachakov, Arina Varlamova, Viktor Svekolkin, Margarita Polyakova, Itzel Valencia, Caitlin Unkenholz, Tania Pannellini, Ilia Galkin, Pavel Ovcharov, Dmitrii Tabakov, Ekaterina Postovalova, Nara Shin, Isha Sethi, Alexander Bagaev, Tomer Itkin, Genevieve Crane, Michael Kluk, Julia Geyer, Giorgio Inghirami, Sanjay Patel
Journal: Blood (2023)
Cold exposure induces vaso-occlusion and pain in sickle mice that depend on complement activation
Authors: Zalaya K. Ivy, John D. Belcher, Iryna A. Khasabova, Chunsheng Chen, Joseph P. Juliette, Fuad Abdulla, Conglin Ruan, Kaje Allen, Julia Nguyen, Victoria M. Rogness, Joan D. Beckman, Sergey G. Khasabov, Kalpna Gupta, Ronald P. Taylor, Donald A. Simone, Gregory M. Vercellotti
Journal: Blood (2023)

Vaso-occlusive pain episodes (VOE) cause severe pain in patients with sickle cell disease (SCD). Vaso-occlusive events promote ischemia/reperfusion pathobiology that activates complement. We hypothesized that complement activation is linked to VOE. We used cold to induce VOE in the Townes sickle homozygous for hemoglobin S (HbSS) mouse model and complement inhibitors to determine whether anaphylatoxin C5a mediates VOE. We used a dorsal skinfold chamber to measure microvascular stasis (vaso-occlusion) and von Frey filaments applied to the plantar surface of the hind paw to assess mechanical hyperalgesia in HbSS and control Townes mice homozygous for hemoglobin A (HbAA) mice after cold exposure at 10°C/50°F for 1 hour. Cold exposure induced more vaso-occlusion in nonhyperalgesic HbSS mice (33%) than in HbAA mice (11%) or HbSS mice left at room temperature (1%). Cold exposure also produced mechanical hyperalgesia as measured by paw withdrawal threshold in HbSS mice compared with that in HbAA mice or HbSS mice left at room temperature. Vaso-occlusion and hyperalgesia were associated with an increase in complement activation fragments Bb and C5a in plasma of HbSS mice after cold exposure. This was accompanied by an increase in proinflammatory NF-κB activation and VCAM-1 and ICAM-1 expression in the liver. Pretreatment of nonhyperalgesic HbSS mice before cold exposure with anti-C5 or anti-C5aR monoclonal antibodies (mAbs) decreased vaso-occlusion, mechanical hyperalgesia, complement activation, and liver inflammatory markers compared with pretreatment with control mAb. Anti-C5 or -C5aR mAb infusion also abrogated mechanical hyperalgesia in HbSS mice with ongoing hyperalgesia at baseline. These findings suggest that C5a promotes vaso-occlusion, pain, and inflammation during VOE and may play a role in chronic pain.
When I use a word . . . Amending the 1972 Poisons Act
Authors: Jeffrey K Aronson
Journal: BMJ (2023)

The 1972 Poisons Act was introduced to enable registered pharmacists, under the aegis of the Royal Pharmaceutical Society, to regulate the sale of non-medicinal poisons and subsequently of explosives precursors. Since then it has undergone several amendments, the latest of which is about to come into force (on 1 October 2023), under The Control of Poisons and Explosives Precursors Regulations 2023, which will introduce additional substances into the lists of currently regulated poisons, as well as precursors of explosives, and will add offences relating to their acquisition, importation, supply, possession, and use.
RANO 2.0: Update to the Response Assessment in Neuro-Oncology Criteria for High- and Low-Grade Gliomas in Adults
Authors: Patrick Y. Wen, Martin van den Bent, Gilbert Youssef, Timothy F. Cloughesy, Benjamin M. Ellingson, Michael Weller, Evanthia Galanis, Daniel P. Barboriak, John de Groot, Mark R. Gilbert, Raymond Huang, Andrew B. Lassman, Minesh Mehta, Annette M. Molinaro, Matthias Preusser, Rifaquat Rahman, Lalitha K. Shankar, Roger Stupp, Javier E. Villanueva-Meyer, Wolfgang Wick, David R. Macdonald, David A. Reardon, Michael A. Vogelbaum, Susan M. Chang
Journal: Journal of Clinical Oncology (2023)

PURPOSE The Response Assessment in Neuro-Oncology (RANO) criteria for high-grade gliomas (RANO-HGG) and low-grade gliomas (RANO-LGG) were developed to improve reliability of response assessment in glioma trials. Over time, some limitations of these criteria were identified, and challenges emerged regarding integrating features of the modified RANO (mRANO) or the immunotherapy RANO (iRANO) criteria. METHODS Informed by data from studies evaluating the different criteria, updates to the RANO criteria are proposed (RANO 2.0). RESULTS We recommend a standard set of criteria for both high- and low-grade gliomas, to be used for all trials regardless of the treatment modalities being evaluated. In the newly diagnosed setting, the postradiotherapy magnetic resonance imaging (MRI), rather than the postsurgical MRI, will be used as the baseline for comparison with subsequent scans. Since the incidence of pseudoprogression is high in the 12 weeks after radiotherapy, continuation of treatment and confirmation of progression during this period with a repeat MRI, or histopathologic evidence of unequivocal recurrent tumor, are required to define tumor progression. However, confirmation scans are not mandatory after this period nor for the evaluation of treatment for recurrent tumors. For treatments with a high likelihood of pseudoprogression, mandatory confirmation of progression with a repeat MRI is highly recommended. The primary measurement remains the maximum cross-sectional area of tumor (two-dimensional) but volumetric measurements are an option. For IDH wild-type glioblastoma, the nonenhancing disease will no longer be evaluated except when assessing response to antiangiogenic agents. In IDH-mutated tumors with a significant nonenhancing component, clinical trials may require evaluating both the enhancing and nonenhancing tumor components for response assessment. CONCLUSION The revised RANO 2.0 criteria refine response assessment in gliomas.
Systemic Therapy for Tumor Control in Metastatic Well-Differentiated Gastroenteropancreatic Neuroendocrine Tumors: ASCO Guideline
Authors: Jaydira Del Rivero, Kimberly Perez, Erin B. Kennedy, Erik S. Mittra, Namrata Vijayvergia, Junaid Arshad, Sandip Basu, Aman Chauhan, Arvind N. Dasari, Andrew M. Bellizzi, Alexandra Gangi, Erin Grady, James R. Howe, Jana Ivanidze, Mark Lewis, Josh Mailman, Nitya Raj, Heloisa P. Soares, Michael C. Soulen, Sarah B. White, Jennifer A. Chan, Pamela L. Kunz, Simron Singh, Thorvardur R. Halfdanarson, Jonathan R. Strosberg, Emily K. Bergsland
Journal: Journal of Clinical Oncology (2023)

To develop recommendations for systemic therapy for well-differentiated grade 1 (G1) to grade 3 (G3) metastatic gastroenteropancreatic neuroendocrine tumors (GEP-NETs).
Laboratory mice with a wild microbiota generate strong allergic immune responses
Authors: Junjie Ma, Egon Urgard, Solveig Runge, Cajsa H. Classon, Laura Mathä, Julian M. Stark, Liqin Cheng, Javiera A. Álvarez, Silvia von Zedtwitz, Austeja Baleviciute, Sergio Martinez Hoyer, Muzhen Li, Anne Marleen Gernand, Lisa Osbelt, Agata Anna Bielecka, Till R. Lesker, Huey-Jy Huang, Susanne Vrtala, Louis Boon, Rudi Beyaert, Mikael Adner, Itziar Martinez Gonzalez, Till Strowig, Juan Du, Susanne Nylén, Stephan P. Rosshart, Jonathan M. Coquet
Journal: Science Immunology (2023)

Allergic disorders are caused by a combination of hereditary and environmental factors. The hygiene hypothesis postulates that early-life microbial exposures impede the development of subsequent allergic disease. Recently developed “wildling” mice are genetically identical to standard laboratory specific pathogen–free (SPF) mice but are housed under seminatural conditions and have rich microbial exposures from birth. Thus, by comparing conventional SPF mice with wildlings, we can uncouple the impact of lifelong microbial exposures from genetic factors on the allergic immune response. We found that wildlings developed larger populations of antigen-experienced T cells than conventional SPF mice, which included interleukin-10–producing CD4 T cells specific for commensal Lactobacilli strains and allergy-promoting T helper 2 (T H 2) cells. In models of airway exposure to house dust mite (HDM), recombinant interleukin-33, or Alternaria alternata , wildlings developed strong allergic inflammation, characterized by eosinophil recruitment, goblet cell metaplasia, and antigen-specific immunoglobulin G1 (IgG1) and IgE responses. Wildlings developed robust de novo T H 2 cell responses to incoming allergens, whereas preexisting T H 2 cells could also be recruited into the allergic immune response in a cytokine-driven and TCR-independent fashion. Thus, wildling mice, which experience diverse and lifelong microbial exposures, were not protected from developing pathological allergic immune responses. Instead, wildlings mounted robust allergic responses to incoming allergens, shedding new light on the hygiene hypothesis.